Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4_0/mira4_de_novo.xml @ 3:a4f602cc3aa9 draft
v0.0.9, was missing mirabait. Adds tests for miraconvert
| author | peterjc |
|---|---|
| date | Fri, 02 Oct 2015 06:12:23 -0400 |
| parents | 4eb32a3d67d1 |
| children | 1713289d9908 |
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| 2:4eb32a3d67d1 | 3:a4f602cc3aa9 |
|---|---|
| 1 <tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.8"> | 1 <tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.9"> |
| 2 <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> | 2 <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="binary">mira</requirement> | 4 <requirement type="binary">mira</requirement> |
| 5 <requirement type="binary">miraconvert</requirement> | 5 <requirement type="binary">miraconvert</requirement> |
| 6 <requirement type="package" version="4.0.2">MIRA</requirement> | 6 <requirement type="package" version="4.0.2">MIRA</requirement> |
| 175 <param name="job_quality" value="accurate" /> | 175 <param name="job_quality" value="accurate" /> |
| 176 <param name="technology" value="sanger" /> | 176 <param name="technology" value="sanger" /> |
| 177 <param name="type" value="none" /> | 177 <param name="type" value="none" /> |
| 178 <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" /> | 178 <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" /> |
| 179 <param name="maf_wanted" value="true"/> | 179 <param name="maf_wanted" value="true"/> |
| 180 <param name="bam_wanted" value="true"/> | 180 <param name="bam_wanted" value="false"/> |
| 181 <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" /> | 181 <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" /> |
| 182 <output name="out_bam" file="empty_file.dat" compare="contains" /> | 182 <output name="out_maf" file="U13small_m.mira4_de_novo.mira" ftype="mira" /> |
| 183 <!-- TODO: Suggest startswith as a compare method? --> | 183 <output name="out_log" file="empty_file.dat" compare="contains" ftype="txt" /> |
| 184 <output name="out_maf" file="header.mira" compare="contains" /> | |
| 185 <output name="out_log" file="empty_file.dat" compare="contains" /> | |
| 186 </test> | 184 </test> |
| 187 <!-- Simple assembly based on MIRA's minidemo/solexa1 example | 185 <!-- Simple assembly based on MIRA's minidemo/solexa1 example |
| 188 Note we're using just one repeat group, | 186 Note we're using just one repeat group, |
| 189 but two parameters within the repeat (filename, no pairing) | 187 but two parameters within the repeat (filename, no pairing) |
| 190 --> | 188 --> |
| 194 <param name="type" value="none" /> | 192 <param name="type" value="none" /> |
| 195 <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" /> | 193 <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" /> |
| 196 <param name="maf_wanted" value="false"/> | 194 <param name="maf_wanted" value="false"/> |
| 197 <param name="bam_wanted" value="false"/> | 195 <param name="bam_wanted" value="false"/> |
| 198 <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" /> | 196 <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" /> |
| 199 <output name="out_log" file="empty_file.dat" compare="contains" /> | 197 <output name="out_log" file="empty_file.dat" compare="contains" ftype="txt" /> |
| 200 </test> | 198 </test> |
| 201 </tests> | 199 </tests> |
| 202 <help> | 200 <help> |
| 203 | 201 |
| 204 **What it does** | 202 **What it does** |